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- PDB-6e6o: Pheromone from Euplotes raikovi, Er-1 -

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Basic information

Entry
Database: PDB / ID: 6e6o
TitlePheromone from Euplotes raikovi, Er-1
ComponentsMating pheromone Er-1/Er-3
KeywordsSIGNALING PROTEIN / PHEROMONE
Function / homology
Function and homology information


pheromone activity / extracellular region / plasma membrane
Similarity search - Function
Pheromone ER-1 / Pheromone Er-1, protozoan / Protozoan pheromone superfamily / Pheromone, protozoan / Euplotes raikovi mating pheromone / Pheromone ER-1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Mating pheromone Er-1/Er-3
Similarity search - Component
Biological speciesEuplotes raikovi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.7 Å
AuthorsFinke, A.D. / Marsh, M.E.
CitationJournal: To Be Published
Title: Ab initio crystal structure determination of Euplotes raikovi pheromones from high-resolution data
Authors: Finke, A.D. / Pedrini, B. / Alimenti, C. / Vallesi, A. / Luporini, P. / Marsh, M.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mating pheromone Er-1/Er-3


Theoretical massNumber of molelcules
Total (without water)4,4181
Polymers4,4181
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.440, 22.560, 23.010
Angle α, β, γ (deg.)90.00, 110.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Mating pheromone Er-1/Er-3 / Euplomone R1/R3


Mass: 4417.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euplotes raikovi (eukaryote) / References: UniProt: P10774
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.47 Å3/Da / Density % sol: 16.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M to 0.2 M (NH4)2SO4, 0.05 M Na Citrate pH 3.5 and 6% (v/v) ethanol, using 5-ul protein drops and 5 ul of reservoir solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.6192 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6192 Å / Relative weight: 1
ReflectionResolution: 0.7→25.02 Å / Num. obs: 39777 / % possible obs: 97 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09503 / Net I/σ(I): 9.41
Reflection shellResolution: 0.7→0.725 Å / Rmerge(I) obs: 1.63 / CC1/2: 0.447

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.7→25.02 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.43 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18445 1989 5 %RANDOM
Rwork0.1654 ---
obs0.16632 37789 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.6 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.895 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å2-0.48 Å2
2--0.43 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 0.7→25.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms303 0 0 22 325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02359
X-RAY DIFFRACTIONr_bond_other_d0.0040.02294
X-RAY DIFFRACTIONr_angle_refined_deg2.6821.961500
X-RAY DIFFRACTIONr_angle_other_deg1.5283.012693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.84126.66718
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4111557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.013151
X-RAY DIFFRACTIONr_chiral_restr0.1190.252
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02442
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0275
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2690.68182
X-RAY DIFFRACTIONr_mcbond_other1.2530.675181
X-RAY DIFFRACTIONr_mcangle_it1.8731.02233
X-RAY DIFFRACTIONr_mcangle_other1.8691.025234
X-RAY DIFFRACTIONr_scbond_it1.5590.838177
X-RAY DIFFRACTIONr_scbond_other1.5560.836177
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0511.217263
X-RAY DIFFRACTIONr_long_range_B_refined2.4638.864453
X-RAY DIFFRACTIONr_long_range_B_other2.4638.847452
X-RAY DIFFRACTIONr_rigid_bond_restr4.3833650
X-RAY DIFFRACTIONr_sphericity_free16.28512
X-RAY DIFFRACTIONr_sphericity_bonded6.3125647
LS refinement shellResolution: 0.7→0.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 139 -
Rwork0.438 2646 -
obs--92.62 %

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